From Ubuntu 18.04 Base Install to Local Run of the KFDRC Alignment Workflow

The following walkthrough begins from a base install of Ubuntu 18.04 LTS (Bionic Beaver) as the root user. The walkthrough will have the users install dependencies, retrieve the most recent workflow, and test the workflow.

Install Dependencies

Step 1: Install python3 and pip3

apt-get update && apt-get -y upgrade

apt-get install -y python3 python3-pip

python3 --version

# Check the version
python3 -m pip --version

# Upgrade pip
python3 -m pip install -U pip

# Check for the upgraded version
python3 -m pip --version

Step 2: Install virtualenv

While not absolutely necessary, it is best practice to use a virtual environment when installing python packages.

python3 -m pip install --user virtualenv

virtualenv -p python3 venv

source venv/bin/activate

Step 3: Install cwltool

Within the virtualenv, we can safely install the cwltool package.

pip install cwlref-runner

cwltool --version

Step 4: Install docker

apt-get install \\
     apt-transport-https \\
     ca-certificates \\
     curl \\
     gnupg-agent \\
     software-properties-common

curl -fsSL <https://download.docker.com/linux/ubuntu/gpg> | apt-key add -

apt-key fingerprint 0EBFCD88

add-apt-repository \\
    "deb [arch=amd64] <https://download.docker.com/linux/ubuntu> \\
    $(lsb_release -cs) \\
    stable"

docker --version

Download the KFDRC Alignment Workflow

Step 1: Get the link for the latest release

The link below is to the latest release for the KFDRC Alignment Workflow:

Release KFDRC Unified Alignment Production Workflow · kids-first/kf-alignment-workflow

Within this link, copy the download URL of the tarball for the next step.

Step 2: Download the latest release

curl -OL <https://github.com/kids-first/kf-alignment-workflow/archive/v2.1.0.tar.gz>

tar xf v2.1.0.tar.gz

cd kf-alignment-workflow-2.1.0/